Allelic distribution at SNP loci within bud dormancy-related QTLs in Japanese apricot (Prunus mume) collections

Bud dormancy broadly affects factors related to tree growth and development, including blooming date and leafing date (LD), which are important phenological traits associated with fruit production. We previously identified significant quantitative trait loci (QTLs) for the leaf bud chilling requirement, heat requirement, and LD on Prunus consensus linkage group 4 (LG4) in Japanese apricot (Prunus mume). However, the significance of QTLs in LG4 for the regulation of dormancy and bud break in diverse P. mume germplasm collections remains undetermined. Accordingly, we first searched for single nucleotide polymorphisms (SNPs) that are in the LG4 QTL interval and associated with LD variations in a segregating F₁ population. We genotyped these SNP loci in 19 P. mume cultivars with a Kompetitive allele-specific PCR genotyping assay. Additionally, we recorded the LD of these collections in the 2016-2017 and 2017-2018 seasons. Our allelic frequency distribution analysis suggested that specific alleles at selected SNP loci that tended to be distributed in late-LD cultivars were not present in early-LD cultivar. However, the early-LD-specific alleles and genotypes of some SNP loci were detected in late-LD cultivars. These results imply that the identified LG4 QTLs for LD is not a single causal determinant of the early-LD phenotype but is one of the loci associated with the LD variation in P. mume germplasm.